rs9513584

chr13-99224027-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001144072.2(UBAC2):c.32-14400G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 152,022 control chromosomes in the GnomAD database, including 26,607 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.57 (26607 hom., cov: 32)
• Consequence: UBAC2 NM_001144072.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.76

Genes affected

UBAC2 (HGNC:20486): (UBA domain containing 2) Involved in negative regulation of canonical Wnt signaling pathway and negative regulation of retrograde protein transport, ER to cytosol. Acts upstream of or within protein localization to endoplasmic reticulum. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UBAC2	NM_001144072.2	c.32-14400G>A		intron_variant		ENST00000403766.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UBAC2	ENST00000403766.8	c.32-14400G>A		intron_variant		2	NM_001144072.2	P1

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86642 AN: 151904 Hom.: 26597 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.572

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.570 AC: 86688 AN: 152022 Hom.: 26607 Cov.: 32 AF XY: 0.564 AC XY: 41890 AN XY: 74280

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.542

Gnomad4 ASJ AF: 0.637

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.629

Gnomad4 NFE AF: 0.710

Gnomad4 OTH AF: 0.570

Alfa AF: 0.638 Hom.: 4386

Bravo AF: 0.557

Asia WGS AF: 0.422 AC: 1470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.0
Dann	Benign	0.82

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9513584; hg19: chr13-99876281;